[2024-01-25 19:53:35,705] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference
[2024-01-25 19:53:36,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,901] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgd88eb7dc-53d4-4366-b0ae-3d28cfe21b13/GCF_012113595.1_ASM1211359v1_genomic.fna.gz | prodigal -d GCF_012113595.1_ASM1211359v1_genomic.fna/cds.fna -a GCF_012113595.1_ASM1211359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:04,596] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:04,596] [INFO] Task started: HMMsearch
[2024-01-25 19:54:04,597] [INFO] Running command: hmmsearch --tblout GCF_012113595.1_ASM1211359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference/reference_markers.hmm GCF_012113595.1_ASM1211359v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:04,954] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:04,956] [INFO] Found 6/6 markers.
[2024-01-25 19:54:05,008] [INFO] Query marker FASTA was written to GCF_012113595.1_ASM1211359v1_genomic.fna/markers.fasta
[2024-01-25 19:54:05,008] [INFO] Task started: Blastn
[2024-01-25 19:54:05,008] [INFO] Running command: blastn -query GCF_012113595.1_ASM1211359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference/reference_markers.fasta -out GCF_012113595.1_ASM1211359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:05,601] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:05,604] [INFO] Selected 20 target genomes.
[2024-01-25 19:54:05,604] [INFO] Target genome list was writen to GCF_012113595.1_ASM1211359v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:05,640] [INFO] Task started: fastANI
[2024-01-25 19:54:05,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgd88eb7dc-53d4-4366-b0ae-3d28cfe21b13/GCF_012113595.1_ASM1211359v1_genomic.fna.gz --refList GCF_012113595.1_ASM1211359v1_genomic.fna/target_genomes.txt --output GCF_012113595.1_ASM1211359v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:26,139] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:26,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:26,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:26,151] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:54:26,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:54:26,151] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	91.1628	1483	2260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	85.2037	869	2260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	85.0848	878	2260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	85.056	875	2260	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	84.9403	886	2260	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	84.7439	1161	2260	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	84.3296	977	2260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	84.2813	968	2260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	84.2674	965	2260	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	84.2212	969	2260	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	83.9562	1183	2260	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	83.9409	1181	2260	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	83.9221	1174	2260	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	83.9173	1172	2260	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	83.885	1177	2260	95	below_threshold
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	83.3223	1020	2260	95	below_threshold
Bacteroides finegoldii	strain=DSM 17565	GCA_000156195.1	338188	338188	suspected-type	True	83.1969	909	2260	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	81.9132	973	2260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:26,152] [INFO] DFAST Taxonomy check result was written to GCF_012113595.1_ASM1211359v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:26,153] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:26,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:26,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference/checkm_data
[2024-01-25 19:54:26,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:26,216] [INFO] Task started: CheckM
[2024-01-25 19:54:26,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012113595.1_ASM1211359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012113595.1_ASM1211359v1_genomic.fna/checkm_input GCF_012113595.1_ASM1211359v1_genomic.fna/checkm_result
[2024-01-25 19:55:40,279] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:40,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:40,304] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:40,304] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:40,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012113595.1_ASM1211359v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:40,305] [INFO] Task started: Blastn
[2024-01-25 19:55:40,305] [INFO] Running command: blastn -query GCF_012113595.1_ASM1211359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01b1729a-2ee7-426f-9656-cc6d3be004a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_012113595.1_ASM1211359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:41,176] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:41,181] [INFO] Selected 9 target genomes.
[2024-01-25 19:55:41,181] [INFO] Target genome list was writen to GCF_012113595.1_ASM1211359v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:41,190] [INFO] Task started: fastANI
[2024-01-25 19:55:41,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgd88eb7dc-53d4-4366-b0ae-3d28cfe21b13/GCF_012113595.1_ASM1211359v1_genomic.fna.gz --refList GCF_012113595.1_ASM1211359v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012113595.1_ASM1211359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:54,116] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:54,123] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:54,124] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_012113595.1	s__Bacteroides sp012113595	100.0	2260	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_903181435.1	s__Bacteroides sp900765785	91.3105	1161	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCA_900761785.1	s__Bacteroides sp900761785	91.2865	1403	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130125.1	s__Bacteroides congonensis	91.1649	1483	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_014750685.1	s__Bacteroides sp014750685	89.1841	1494	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001688725.2	s__Bacteroides caecimuris	85.0881	871	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_002222615.2	s__Bacteroides caccae	84.2162	966	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_001314995.1	s__Bacteroides ovatus	83.9003	1175	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_000374365.1	s__Bacteroides gallinarum	77.9447	281	2260	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:54,125] [INFO] GTDB search result was written to GCF_012113595.1_ASM1211359v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:54,126] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:54,129] [INFO] DFAST_QC result json was written to GCF_012113595.1_ASM1211359v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:54,129] [INFO] DFAST_QC completed!
[2024-01-25 19:55:54,129] [INFO] Total running time: 0h2m18s